RetrogeneDB ID: retro_cjac_4005

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL287771.1:2..1030(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSCJAG00000014091
• Aliases: None
• Description: None

Sequence

>retro_cjac_4005
AAGTGGCCAATCTGCCATGGTACAGTTGAATATTGGGACTTGATGTAAAGGTTTATGGAGCAAGTGATCGTTAAATATTT
AAGGGAAAAACCTGAAGACTATTATTTTCTCTTGACTGAACTTCCATTGAATACTCCAGAAAACAGGGAATATACTGCTG
AAATAATGTTTGAATCTTTCAATGTTCCAGGCTTGTACATTGCTGTGCAGGCTGTTCTTGCCTTAGCTACATCTTGGACC
TCAAGAAAAGTAGGAGAACGGACATTGACTGGTATGGTAATAGATAGTGGAGATGGTGTCACTCATGTCATTCCTGTGGC
TGAAGGGTATGTGAAGGGTTATATTAAACACATTCCAATCACAGGATGAGATATAACATATTTTAATCAGGAACTGCTGA
GAGACCAATAAGTAGGAATCCCTCCAGAACAATCTTTGGAAACTGGCAAGGCAGTAAAGGAGTGCTATAGTTACGTCTGC
CCAGATTTAGTGAAAGAATTTAACAAGTATGATACAGATGGGTCAAAACGGATTAAACCGTATACTGGAATCAATGCTAT
CTCAAAGAAAGAATTTTCAGTTGATGTTGGTTATGAGAGATTTTTTGGACCTGAAATCTTTTTTCATCCAGAGTTTTCTA
ATCCAGACTTTACACAACCTATCTCAGAAGTTGTAGATGAAGTAATTTAGAATTGTCCTGTTGATGTCAGACATCATCTC
TACAAAAATATTGTCCTCTCTGGAGGTTCAACCATGTTCAGGGAATTTGCACATCACTTGCAAAGAGATTTAAAAAGAAC
TGTAGATGCCCGGCTGAAATTAAGTGAGGAATTTAGTGGTGGTAAATTAAAGCCATAACCTATTGATGTACAAGTCATTA
CACACCACATGCAGAAATATGCAGTTTGGTTTGGAGGATTAGTTCTGGCTTCCACACCTGAGTTCTACCAATTATGCCAC
ACCAAAAAGGATTATAAAAAATTGGACCTAGCATTTGTCGTCACAATCCAGTGTTTGGAGTCATGTCA

Alignment

ORF - retro_cjac_4005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 82.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQ
          KWPI.HG.VE.WDLM.RFMEQVI.KYLR..PED.YFLLTE.PLNTPENREYTAEIMFESFNVPGLYIAVQ
Retrocopy KWPICHGTVEYWDLM*RFMEQVIVKYLREKPEDYYFLLTELPLNTPENREYTAEIMFESFNVPGLYIAVQ

Parental  AVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVG
          AVLALA.SWTSR.VGERTLTG.VIDSGDGVTHVIPVAEGYV.G..IKHIPI.G.DITYF.Q.LLRD..VG
Retrocopy AVLALATSWTSRKVGERTLTGMVIDSGDGVTHVIPVAEGYVKGY-IKHIPITG*DITYFNQELLRDQ*VG

Parental  IPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFH
          IPPEQSLET.KAVKE.YSYVCPDLVKEFNKYDTDGSK.IK.YTGINAISKKEFS.DVGYERF.GPEIFFH
Retrocopy IPPEQSLETGKAVKECYSYVCPDLVKEFNKYDTDGSKRIKPYTGINAISKKEFSVDVGYERFFGPEIFFH

Parental  PEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELS
          PEF.NPDFTQPISEVVDEVI.NCP.DVR..LYKNIVLSGGSTMFR.F...LQRDLKRTVDARLKLSEE.S
Retrocopy PEFSNPDFTQPISEVVDEVI*NCPVDVRHHLYKNIVLSGGSTMFREFAHHLQRDLKRTVDARLKLSEEFS

Parental  GGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYE-EIGPSICRHNPVFGVMS
          GG.LKP.PIDVQVITHHMQ.YAVWFGG..LASTPEFYQ.CHTKKDY...IGPSICRHNPVFGVMS
Retrocopy GGKLKP*PIDVQVITHHMQKYAVWFGGLVLASTPEFYQLCHTKKDYK<KIGPSICRHNPVFGVMS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	183.47 RPM
SRP051959_heart	0.00 RPM	46.78 RPM
SRP051959_kidney	0.00 RPM	67.07 RPM
SRP051959_liver	0.00 RPM	47.96 RPM
SRP051959_lung	0.00 RPM	112.70 RPM
SRP051959_lymph_node	0.00 RPM	176.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.63 RPM
SRP051959_spleen	0.00 RPM	146.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4005 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4005 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4005 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005 ,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,